Is this your own experience?
I have never had any problems because of stretching after running, it feels very good, it takes the tension out of my muscles, loosens them. I've met another runner, and we did that after running automatically. Rhythm: 20 secs, short pause and 20 secs again.
Whose theory is that? My source of information (book "Ernaehrung und Training" by Dr. W. Feil and Dr. T. Wessinghage [european champion over 5000m in 1982]) clearly states, that "stretching [immediately after sport] is the gate of regeneration".